Transcriptomics

Training material for all kinds of transcriptomics analysis.

Requirements

Before diving into this topic, we recommend you to have a look at:

Material

Lesson Slides Hands-on Input dataset Workflows Galaxy tour Galaxy instances
Introduction to Transcriptomics
slides
CLIP-Seq data analysis from pre-processing to motif detection
tutorial zenodo_link workflow interactive_tour
De novo transcriptome reconstruction with RNA-Seq
tutorial zenodo_link workflow interactive_tour
Differential abundance testing of small RNAs
tutorial zenodo_link workflow interactive_tour
Downstream Single-cell RNA analysis with RaceID
single-cell
tutorial zenodo_link workflow
GO Enrichment Analysis
tutorial zenodo_link workflow
Network analysis with Heinz
metatranscriptomics network analysis
slides tutorial zenodo_link workflow interactive_tour
Plates, Batches, and Barcodes
single-cell
slides
Pre-processing of 10X Single-Cell RNA Datasets
single-cell 10x
tutorial zenodo_link workflow
Pre-processing of Single-Cell RNA Data
single-cell
tutorial zenodo_link workflow
RNA Seq Counts to Viz in R
tutorial zenodo_link
RNA-Seq reads to counts
collections mouse QC
tutorial zenodo_link workflow
RNA-seq counts to genes
limma-voom mouse QC
tutorial zenodo_link workflow
RNA-seq genes to pathways
mouse
tutorial zenodo_link workflow
Reference-based RNA-Seq data analysis
bulk rna-seq
tutorial zenodo_link workflow interactive_tour
Single-cell quality control with scater
single-cell
tutorial zenodo_link workflow
Small Non-coding RNA Clustering using BlockClust
tutorial zenodo_link workflow
Understanding Barcodes
single-cell
tutorial zenodo_link
Visualization of RNA-Seq results with CummeRbund
slides tutorial zenodo_link interactive_tour
Visualization of RNA-Seq results with Volcano Plot
tutorial zenodo_link workflow
Visualization of RNA-Seq results with heatmap2
tutorial zenodo_link workflow

Galaxy instances

You can use a public Galaxy instance which has been tested for the availability of the used tools. They are listed along with the tutorials above.

Maintainers

This material is maintained by:

Bérénice BatutBérénice Batut, Maria DoyleMaria Doyle

For any question related to this topic and the content, you can contact them or visit our Gitter channel.

Contributors

This material was contributed to by:

Bérénice BatutBérénice Batut, Anika ErxlebenAnika Erxleben, Markus WolfienMarkus Wolfien, Florian HeylFlorian Heyl, Daniel MaticzkaDaniel Maticzka, Mallory FreebergMallory Freeberg, Mo HeydarianMo Heydarian, Mehmet TekmanMehmet Tekman, Alex OstrovskyAlex Ostrovsky, IGC Bioinformatics UnitIGC Bioinformatics Unit, Maria DoyleMaria Doyle, Chao (Cico) ZhangChao (Cico) Zhang, Hans-Rudolf HotzHans-Rudolf Hotz, Daniel BlankenbergDaniel Blankenberg, Wolfgang MaierWolfgang Maier, Fotis E. PsomopoulosFotis E. Psomopoulos, Toby HodgesToby Hodges, Belinda PhipsonBelinda Phipson, Harriet DashnowHarriet Dashnow, Jovana MaksimovicJovana Maksimovic, Anna TrigosAnna Trigos, Matt RitchieMatt Ritchie, Shian SuShian Su, Charity LawCharity Law, Pavankumar VidemPavankumar Videm, Clemens BlankClemens Blank, Nicola SoranzoNicola Soranzo, Peter van HeusdenPeter van Heusden, Graham EtheringtonGraham Etherington, Andrea BagnacaniAndrea Bagnacani

References